Comparing whole-genome sequencing to pulsed-field gel electrophoresis for vancomycin-resistant Enterococcus faecium hospital surveillance

Vancomycin-resistant enterococci (VREs) have emerged as an important public health concern and a leading cause of healthcare-associated infections. Accurately distinguishing between closely related VRE strains is imperative for infection control measures in the setting of hospital outbreaks. Although pulsed-field gel electrophoresis (PFGE) is considered the gold standard for VRE strain typing, recent studies have identified whole-genome sequencing (WGS) as a promising alternative with greater resolution. In this study, we report on the validation and utility of a WGS and single-nucleotide polymorphism (SNP) analysis pipeline toward vancomycin-resistant Enterococcus faecium (VREfm) strain typing in a large academic medical center. Using PFGE as the reference method, we identified a conservative threshold of ≤10 SNPs as robustly identifying related VREfm isolates with 98.5% sensitivity and 93.1% specificity. Comparing VREfm infection control surveillance pre- and post-WGS SNP strain typing revealed a proportionally greater number of isolates with related strain types and epidemiological links in the post-WGS SNP group. These findings suggest that WGS SNP analysis can improve the resolution of emerging hospital outbreaks and infection control measures, as compared to PFGE. IMPORTANCE Distinguishing between closely related antibiotic-resistant bacteria is an important task toward infection control measures in a hospital environment. This study focused on strains of one particular antibiotic-resistant bacterium (vancomycin-resistant Enterococcus faecium ) and assessed the utility of a whole-genome sequencing analysis pipeline toward distinguishing strain relatedness compared to the gold standard reference method. The results showed that strain typing with whole-genome sequencing identified a proportionally greater number of transmission/outbreak events compared to the reference method over a similar time period. The findings suggest that a whole-genome sequencing pipeline, when available, can improve hospital infection control measures.